++ed by:
MAJENSEN CJFIELDS GENEHACK THALJEF FIBO

5 PAUSE user(s)
6 non-PAUSE user(s).

Christopher Fields
and 1 contributors

NAME

Bio::Align::Graphics - Graphic Rendering of Bio::Align::AlignI Objects

SYNOPSIS

  use Bio::Align::Graphics;

  #Get an AlignI object, usually by using Bio::AlignIO

  my $file=shift @ARGV;
  my $in=new Bio::AlignIO(-file=>$file, -format=>'clustalw');
  my $aln=$in->next_aln();


  #Create a new Graphics object
  my $print_align = new Bio::Align::Graphics(align => $aln);

  #Draw the alignment
  $print_align->draw();

DESCRIPTION

Bio::Align::Graphics is a module designed to create image files out of Bio::Align::AlignI objects. An alignment may be manipulated with various formatting and highlighting options.

An example:

        #!/usr/bin/perl -w

        use Bio::AlignIO;
        use Bio::Align::Graphics;
        use strict;
        
        #Get an alignment file
        my $file = shift @ARGV;
        
        #Create an AlignI object using AlignIO
        my $in=new Bio::AlignIO(-file=>$file, -format=>'clustalw');

        #Read the alignment
        my $aln=$in->next_aln();

        #Create some domains for highlighting
        my @domain_start = ( 25 , 50, 80 );
        my @domain_end = ( 40 , 60 , 100 );
        my @domain_color = ( 'red' , 'cyan' , 'green' );
        
        #Create Labels for the domains
        my @dml = ("CARD", "Proline Rich", "Transmembrane");
        my @dml_start = (25, 50, 80);
        my @dml_end = (40, 60, 100);
        my @dml_color = ("lightpink", "lightblue", "lightgreen");
        
        
        #Create individual labels
        my %labels = ( 145 => "Hep-c target");
        
        
        my $print_align = new Bio::Align::Graphics( align => $aln,
                                        pad_bottom => 5,
                                        domain_start => \@domain_start,
                                        domain_end => \@domain_end,
                                        dm_color => \@domain_color,
                                        dm_labels => \@dml,
                                        dm_label_start => \@dml_start,
                                        dm_label_end => \@dml_end,
                                        dm_label_color => \@dml_color,
                                        labels => \%labels,
                                        out_format => "png");
                                        
        $print_align->draw();

METHODS

This section describes the class and object methods for Bio::Align::Graphics.

Typically you will begin by creating a Bio::Align::Graphics object, passing it an alignment object created using Bio::AlignIO. The Bio::Align::Graphics->new() method has a number of configuration variables that allow you to control the appearance of the final image.

You will then call the draw() method to output the final image.

CONSTRUCTORS

new() is the constructor for Bio::Align::Graphics:

The new() method creates a new graphics object. The options are a set of tag/value pairs as follows:

  Option         Value                                  Default
  ------         -----                                  -------

  align          Bio::AlignI object                     None, must be 
                                                        supplied to draw
                                                        an alignment

  output         Filename to print image to             STDOUT

  out_format     png, jpeg, gif, gd                     png

  font           Size of font, ranging from 1 to 5      2
                 and equal to the standard GD fonts
                 ranging from gdTinyFont to 
                 gdGiantFont

  x_label        Draws a scale numbering alignment      true
                 bases along top of image, every x
                 bases are numbered, where x is the
                 block_size option

  y_label        Draws sequence ids of alignment        true
                 along left side of image

  bg_color       Background color of the image          white

  font_color     Color of the font used for drawing     black
                 the alignment characters

  x_label_color  Color of the font used for drawing     red
                 the base scale characters

  y_label_color  Color of the font used for drawing     blue
                 the sequence id characters

  p_color        Colors protein bases according to      false
                 a coloring scheme proposed by W.R.
                 Taylor(Protein Engineering, vol 10
                 no 7, 1997), only works with
                 protein alignments

  pad_top        Additional whitespace characters       5
                 between top of image and x-label

  pad_bottom     Additional whitespace characters       5
                 between bottom of image and
                 alignment

  pad_left       Additional whitespace characters       5
                 between left side of image and 
                 y-label

  pad_right      Additional whitespace characters       5
                 between right side of image and 
                 alignment

  x_label_space  Additional whitespace characters       1
                 between x_label and alignment

  y_label_space  Additional whitespace characters       1
                 between y_label and alignment

  reference      Characters which are identical to      false
                 the reference sequence are replaced
                 with the match character

  reference_id   Sequence id of the sequence to use     First sequence
                 as the reference                       supplied in alignment

  match_char     Character to replace identical bases   .
                 in aligned sequences

  block_size     Number of bases to group together      10
                 when printing alignment, groups are
                 separated by whitespace

  block_space    Amount of character whitespace to      2
                 separate groups of bases by

  labels         A hash containing labels to be         none
                 printed beneath the alignment, 
                 where the keys are the bases to
                 print the values at

  dm_start       An array containing start bases        none
                 for highlighting of segments of
                 the alignment, paired with dm_end
                 option

  dm_end         An array containing end bases          none
                 for highlighting of segments of
                 the alignment, paired with dm_start
                 options

  dm_color       An array containing colors for         silver
                 highlighting segments of bases
                 denoted by the coordinates
                 located in the dm_start and dm_end
                 options

  dml_start      An array containing start bases        none
                 for addition of domain labels
                 underneath the alignment, paired
                 with dml_end

  dml_end        An array containing end bases          none
                 for addition of domain labels
                 underneath the alignment, paired
                 with dml_start

  dml_color      An array containing colors for         silver
                 the domain labels denoted by the
                 coordinates located in the 
                 dml_start and dml_end options

  dm_labels      An array containing labels to be       none
                 printed underneath specified
                 domains, each label should
                 correspond with the base position
                 located in the dml_start option
                 
  show_nonsynonymous  Boolean value to turn option      false
                 on or off. If 0 (or undef), option
                 is off. If 1 (or non-0), option is on.
                 Only valid for nucleotide alignments.
                 Output images are wider with this option on.

Note that all arrays and hashes must be passed by reference.

OBJECT METHODS

$draw_align->draw();

The draw() method draws the image with the options that were specified with new().

$draw_align->width();

Get the width of the image created with new(), in pixels.

$draw_align->height();

Get the height of the image created with new(), in pixels.

$draw_align->aln_length();

Get the length of the alignment submitted to new().

$draw_align->aln_format();

Get the format of the alignment submitted to new().

$draw_align->no_sequences();

Get the number of sequences in the alignment submitted to new().

AUTHORS AND CONTRIBUTORS

William McCaig, <wmccaig@gmail.com>

Mikhail Bekarev, <mbekarev@hunter.cuny.edu>

Yözen Hernández, <yzhernand@gmail.com>

Weigang Qiu (Corresponding Developer), <weigang@genectr.hunter.cuny.edu>

COPYRIGHT AND LICENSE

Copyright (C) 2006-2008 by William McCaig

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.3 or, at your option, any later version of Perl 5 you may have available.

SEE ALSO

Bio::Align::AlignI, Bio::AlignIO, GD, GD::Simple